Well, there are two points here. First off, what the RC church may have done in the Middle Ages is somewhat different since the culture was different as well. The idea of human rights didn't exist at the time and wouldn't exist for centuries afterwards. The Romans fed people to lions, does that mean that we should look sideways at the Italians whenever they quote history? Slavery was practiced in America until a little over a century ago. Does that mean that the US can never take a stance on slavery?
We live and we grow. Even the Church does. Any political body which has existed as long as the RC church has lots of skeletons in its closet. That doesn't mean that it cannot take a stance on current affairs. Sure, the RC church has lots of blood on its hands. But, it hasn't done that for quite some time. You could make the arguement that they didn't know any better since no one else was particularly interested in treating eachother decently at the time either.
What's the excuse for the radical Islamic groups? They haven't taken a history class?
/edit - whoops, forgot my second point. :/
The second point is that that the context is being entirely ignored by the media. This was a scholorly debate, not a public forum. These were historians discussing issues. Now, I believe that the Pope has made a serious error in thinking that anything he says is private, but, I do believe that these comments were not intended the way they have been taken.
